fix: add biofvm into reactions_diffusion namespace

reactions-diffusion/biofvm/examples/diffuse.cpp

@@ -10,7 +10,7 @@
 #include <biofvm/microenvironment.h>
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
 int main()
 {

reactions-diffusion/biofvm/include/biofvm/agent.h

@@ -3,8 +3,8 @@
 #include "agent_data.h"
 #include "agent_generic_storage.h"
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 using agent = agent_generic_storage<base_agent_data, agent_data>;
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm

reactions-diffusion/biofvm/include/biofvm/agent_container.h

@@ -5,10 +5,10 @@
 
 #include "agent.h"
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 using agent_container = physicore::generic_agent_and_data_container<base_agent, agent>;
 using agent_container_interface = physicore::generic_agent_interface_container<agent_interface>;
 using container_ptr = std::shared_ptr<agent_container_interface>;
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm

reactions-diffusion/biofvm/include/biofvm/agent_data.h

@@ -2,7 +2,7 @@
 
 #include "agent_data_generic_storage.h"
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 using agent_data = agent_data_generic_storage<std::vector>;
 

reactions-diffusion/biofvm/include/biofvm/agent_data_generic_storage.h

@@ -5,7 +5,7 @@
 #include <common/base_agent_data.h>
 #include <common/types.h>
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 template <template <typename...> typename ContainerType = std::vector>
 struct agent_data_generic_storage
@@ -109,4 +109,4 @@ void agent_data_generic_storage<ContainerType>::remove_at(index_t position)
 	is_active.resize(agents_count);
 }
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm

reactions-diffusion/biofvm/include/biofvm/agent_generic_storage.h

@@ -5,7 +5,7 @@
 
 #include "agent_interface.h"
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 #ifdef _MSC_VER
 	#pragma warning(push)
@@ -79,4 +79,4 @@ class agent_generic_storage : public physicore::base_agent_generic_storage<BaseA
 	#pragma warning(pop)
 #endif
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm

reactions-diffusion/biofvm/include/biofvm/agent_interface.h

@@ -3,7 +3,7 @@
 #include <common/base_agent_interface.h>
 #include <common/types.h>
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 class agent_interface : public virtual base_agent_interface
 {
@@ -27,4 +27,4 @@ class agent_interface : public virtual base_agent_interface
 	virtual uint8_t& is_active() = 0;
 };
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm

reactions-diffusion/biofvm/include/biofvm/bulk_functor.h

@@ -3,7 +3,7 @@
 #include <biofvm/biofvm_export.h>
 #include <common/types.h>
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 struct BIOFVM_EXPORT bulk_functor
 {
@@ -13,4 +13,4 @@ struct BIOFVM_EXPORT bulk_functor
 	virtual ~bulk_functor() = default;
 };
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm

reactions-diffusion/biofvm/include/biofvm/mesh.h

@@ -6,7 +6,7 @@
 #include <biofvm/biofvm_export.h>
 #include <common/types.h>
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 struct BIOFVM_EXPORT cartesian_mesh
 {
@@ -31,4 +31,4 @@ struct BIOFVM_EXPORT cartesian_mesh
 	std::array<real_t, 3> voxel_center(std::array<index_t, 3> position) const;
 };
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm

reactions-diffusion/biofvm/include/biofvm/microenvironment.h

@@ -15,7 +15,7 @@
 #include "serializer.h"
 #include "solver.h"
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 class BIOFVM_EXPORT microenvironment : public timestep_executor
 {
@@ -81,4 +81,4 @@ class BIOFVM_EXPORT microenvironment : public timestep_executor
 	bool compute_internalized_substrates = false;
 };
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm

reactions-diffusion/biofvm/include/biofvm/microenvironment_builder.h

@@ -9,7 +9,7 @@
 #include "mesh.h"
 #include "microenvironment.h"
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 class BIOFVM_EXPORT microenvironment_builder
 {
@@ -77,4 +77,4 @@ class BIOFVM_EXPORT microenvironment_builder
 	std::unique_ptr<microenvironment> build();
 };
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm

reactions-diffusion/biofvm/include/biofvm/serializer.h

@@ -4,7 +4,7 @@
 #include <biofvm/biofvm_export.h>
 #include <common/types.h>
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 class microenvironment;
 
@@ -18,4 +18,4 @@ class BIOFVM_EXPORT serializer
 
 using serializer_ptr = std::unique_ptr<serializer>;
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm

reactions-diffusion/biofvm/include/biofvm/solver.h

@@ -5,7 +5,7 @@
 #include <biofvm/biofvm_export.h>
 #include <common/types.h>
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 class microenvironment;
 
@@ -38,4 +38,4 @@ class BIOFVM_EXPORT solver
 
 using solver_ptr = std::unique_ptr<solver>;
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm

reactions-diffusion/biofvm/include/biofvm/solver_registry.h

@@ -8,7 +8,7 @@
 
 #include "solver.h"
 
-namespace physicore::biofvm {
+namespace physicore::reactions_diffusion::biofvm {
 
 class solver_registry
 {
@@ -38,4 +38,4 @@ struct registry_adder
 	}
 };
 
-} // namespace physicore::biofvm
+} // namespace physicore::reactions_diffusion::biofvm

reactions-diffusion/biofvm/kernels/openmp_solver/examples/benchmark.cpp

@@ -10,8 +10,8 @@
 #include "dirichlet_solver.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 namespace {
 void make_agents(microenvironment& m, index_t count, bool conflict)

reactions-diffusion/biofvm/kernels/openmp_solver/include/openmp_solver/register_solver.h

@@ -1,6 +1,6 @@
 #pragma once
 
-namespace physicore::biofvm::kernels::openmp_solver {
+namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver {
 
 void attach_to_registry();
 

reactions-diffusion/biofvm/kernels/openmp_solver/src/bulk_solver.cpp

@@ -3,8 +3,8 @@
 #include <noarr/structures_extended.hpp>
 
 using namespace physicore;
-using namespace physicore::biofvm;
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 void bulk_solver::initialize(microenvironment& m) { fnc = std::move(m.bulk_fnc); }
 

reactions-diffusion/biofvm/kernels/openmp_solver/src/bulk_solver.h

@@ -15,7 +15,7 @@ D = (D + dt*S*T)/(1 + dt*(U+S))
 where D is a voxel substrate density vector
 */
 
-namespace physicore::biofvm::kernels::openmp_solver {
+namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver {
 
 class bulk_solver
 {
@@ -27,4 +27,4 @@ class bulk_solver
 	void solve(const microenvironment& m, diffusion_solver& d_solver);
 };
 
-} // namespace physicore::biofvm::kernels::openmp_solver
+} // namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver

reactions-diffusion/biofvm/kernels/openmp_solver/src/cell_solver.cpp

@@ -5,8 +5,8 @@
 #include <noarr/structures_extended.hpp>
 
 using namespace physicore;
-using namespace physicore::biofvm;
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 
 namespace {

reactions-diffusion/biofvm/kernels/openmp_solver/src/cell_solver.h

@@ -38,7 +38,7 @@ F = fraction released at death
 D = D + I*F/v
 */
 
-namespace physicore::biofvm::kernels::openmp_solver {
+namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver {
 
 class cell_solver : private generic_agent_solver<agent>
 {
@@ -68,4 +68,4 @@ class cell_solver : private generic_agent_solver<agent>
 	void release_internalized_substrates(const microenvironment& m, diffusion_solver& d_solver, index_t index);
 };
 
-} // namespace physicore::biofvm::kernels::openmp_solver
+} // namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver

reactions-diffusion/biofvm/kernels/openmp_solver/src/diffusion_solver.cpp

@@ -8,7 +8,7 @@
 #include "solver_utils.h"
 
 using namespace physicore;
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 namespace {
 auto get_diagonal_layout(const problem_t& problem, index_t n)

reactions-diffusion/biofvm/kernels/openmp_solver/src/diffusion_solver.h

@@ -39,7 +39,7 @@ d_i'' == (d_i' + c_i*d_(i+1)'')*b_i'                          n >  i >= 1
 y/z dimensions are solved alongside tiled xs dimension
 */
 
-namespace physicore::biofvm::kernels::openmp_solver {
+namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver {
 
 class diffusion_solver
 {
@@ -92,4 +92,4 @@ class diffusion_solver
 	void solve();
 };
 
-} // namespace physicore::biofvm::kernels::openmp_solver
+} // namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver

reactions-diffusion/biofvm/kernels/openmp_solver/src/dirichlet_solver.cpp

@@ -4,8 +4,8 @@
 #include "omp_helper.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 namespace {
 auto fix_dims(const index_t* voxel_index, index_t dims)

reactions-diffusion/biofvm/kernels/openmp_solver/src/dirichlet_solver.h

@@ -12,12 +12,12 @@ m.dirichlet_conditions - array of bools specifying if a substrate of a dirichlet
 m.dirichlet_values - array of dirichlet values for each substrate with a dirichlet condition
 */
 
-namespace physicore::biofvm::kernels::openmp_solver {
+namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver {
 
 class dirichlet_solver
 {
 public:
 	static void solve(microenvironment& m, diffusion_solver& d_solver);
 };
 
-} // namespace physicore::biofvm::kernels::openmp_solver
+} // namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver

reactions-diffusion/biofvm/kernels/openmp_solver/src/openmp_solver.cpp

@@ -3,7 +3,7 @@
 #include "dirichlet_solver.h"
 
 using namespace physicore;
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 void openmp_solver::initialize(biofvm::microenvironment& m)
 {

reactions-diffusion/biofvm/kernels/openmp_solver/src/openmp_solver.h

@@ -6,7 +6,7 @@
 #include "cell_solver.h"
 #include "diffusion_solver.h"
 
-namespace physicore::biofvm::kernels::openmp_solver {
+namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver {
 
 class openmp_solver : public solver
 {
@@ -26,4 +26,4 @@ class openmp_solver : public solver
 	void recompute_positional_data(microenvironment& m) override;
 };
 
-} // namespace physicore::biofvm::kernels::openmp_solver
+} // namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver

reactions-diffusion/biofvm/kernels/openmp_solver/src/problem.h

@@ -4,7 +4,7 @@
 
 #include <biofvm/microenvironment.h>
 
-namespace physicore::biofvm::kernels::openmp_solver {
+namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver {
 
 struct problem_t
 {
@@ -46,4 +46,4 @@ struct problem_t
 	}
 };
 
-} // namespace physicore::biofvm::kernels::openmp_solver
+} // namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver

reactions-diffusion/biofvm/kernels/openmp_solver/src/register_solver.cpp

@@ -4,7 +4,8 @@
 
 #include "openmp_solver.h"
 
-void physicore::biofvm::kernels::openmp_solver::attach_to_registry()
+void physicore::reactions_diffusion::biofvm::kernels::openmp_solver::attach_to_registry()
 {
-	static const physicore::biofvm::registry_adder<openmp_solver> openmp_solver_adder("openmp_solver");
+	static const physicore::reactions_diffusion::biofvm::registry_adder<openmp_solver> openmp_solver_adder(
+		"openmp_solver");
 }

reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_bulk_solver.cpp

@@ -6,9 +6,9 @@
 #include "diffusion_solver.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 namespace {
 std::unique_ptr<microenvironment> default_microenv(cartesian_mesh mesh)

reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_cell_solver.cpp

@@ -8,9 +8,9 @@
 #include "diffusion_solver.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 namespace {
 std::unique_ptr<microenvironment> default_microenv(cartesian_mesh mesh, bool compute_interalized)

reactions-diffusion/biofvm/kernels/openmp_solver/tests/test_diffusion_solver.cpp

@@ -4,9 +4,9 @@
 #include "diffusion_solver.h"
 
 using namespace physicore;
-using namespace physicore::biofvm;
+using namespace physicore::reactions_diffusion::biofvm;
 
-using namespace physicore::biofvm::kernels::openmp_solver;
+using namespace physicore::reactions_diffusion::biofvm::kernels::openmp_solver;
 
 namespace {
 std::unique_ptr<microenvironment> default_microenv(cartesian_mesh mesh)